September 13, 2012

Italian and Sardinian autosomal genetics

Cornelia di Gaetano et al., An Overview of the Genetic Structure within the Italian Population from Genome-Wide Data. PLoS ONE, 2012. Open access ··> LINK[doi:10.1371/journal.pone.0043759]

The results confirm that Sardians are a very distinct population and show that Italians essentially seem to cluster with mainland Europeans (NW Europeans in principle but Iberian or Balcanic comparisons are missing), West Asians and Sardinians in this order.

There is some N-S gradient in the Peninsula and Sicily but it's mostly determined by an increasing West Asian affinity in the South. Central Italians stand between North and South but clearly closer to the North but many individuals from NW Italy (Liguria and Piedmont, as well as some Sardinians) actually cluster with Southern Italians as well as with "mixed" Sardinians (those Sardinians who stand between the main insular cluster and the peninsular one).

Let's see:

Figure 1. SNP-Based PC of 1,262 individuals from 10 sub-populations.
The Italian population plotted onto the first two principal components defined by the European HGDP-CEPH populations and CEU HapMap data. Scatter plot of the first two principal components, obtained using R software (prcomp). Analysis based on 125,799 autosomal SNPs. Individuals included belong to Northern Italy (N-IT): black dots, Central Italy (C-IT): red dots, Southern Italy (S-IT): green dots, Sardinian (SAR): blue dots... [the original legend does not explain well the other populations (too many blatant errors in the text) but it's obvious that the group to the top-right corner are other Europeans (French, CEU), while the group to the center-left are West Asians (Druze, Palestinian, Bedouins) and Mozabites. Larger images can be downloaded from the paper].

In this first characterization we see a primary duality between Europe and West Asia (the Paleo-Neolithic dichotomy probably) and a secondary one between Sardinia and mainland Europe.

Figure 2. SNP-Based PC of 1,014 individuals from the Italian dataset.
A. A Scatter Plot of the Italian population of the first two principal components obtained via R software (prcomp). Individuals included belong to Northern Italy : black dots, Central Italy : red dots, Southern Italy : green dots, Sardinian: blue dots.
B. Italian population without the Sardinian-projected scatter plot of the first two principal components obtained via the R software (prcomp)[larger images can be downloaded from the paper]

Here we see (A) a main dichotomy between Sardinia and Peninsular Italy (with Sicily) and a secondary N-S gradient. However in (B) it becomes more obvious that to some extent there are two distinct clusters: Southern and Central-North Italy with certain clear separation.

However, and this is quite interesting some North Italians strongly cluster with Southern Italians. Razib mentions this fact as signature of internal Italian migrations but individual migrations would not look that way because the genetic distinction would have diluted in the meantime, appearing at most as intermediate. What we see instead is preserved genetic identity, not too diluted or not diluted at all, with Southern Italy in many Northern Italians.

Who are these Northern Italians, I wondered then. The answer is in the supplements:

Hidden population structure within the Italian dataset. Scatter plot of the first two eigenvectors based on 125,799 autosomal SNPs and 1,012 individuals. Colors represent the four different macro-areas; green- Southern Italy (Apulia, Calabria/Sicily, Campania, Basilicata), red- Central Italy (Tuscany, Lazio, Emilia Romagna and Abruzzo/Marche), black- Northern Italy (Piedmont,Liguria, Aosta Valley and Lombardy), blue- Sardinia (these samples were labeled for the linguistic area). Subjects are symbol- labeled by municipality. Information on municipality was not used for calculations.

[click to expand]

In this image we can appreciate how all Northern Italians clustering with Southern Italians are from two specific regions: Liguria and Piedmont (Piemonte), the Northwestern regions of Italy, bordering France. What do these two regions have in common? All I can think is that, in ancient times they were mostly inhabited by the Ligures, a pre-Indoeuropean people plausibly descendant from the first Neolithic colonization (Cardium Pottery, via the Chassey-Cortaillod-La Lagozza cultural complex).

Roman region of Liguria (Regio IX)

We are also provided with a bayesian cluster analysis, for which K=4 seems the most valid result (K=3 and K=5 also give low cross-validation values but do not seem more informative):

Figure 3. Clustering of the European, Northern African and Middle Eastern individuals by the Structure software.
Model-based
ancestry analysis based on a subset of HGDP-CEPH and HapMap CEU data
using the merged data of 126K autosomal SNPs. Ancestry for each
individual was inferred using ADMIXTURE [50] at K = 4. Abbreviations as in Figure 1.

This confirms four clusters: Main European (green), Sardinian (red), West Asian (blue) and North African (purple).

I tend to consider the West Asian component as the main Neolithic input in Europe, although, of course other DNA sections may well have traveled around in that period or later on.

I also find notable that Sardinian affinity exists among Italians, French and North Africans (surely via Iberia) but almost not among North American Euro-descendants (CEU) of NW European origin and West Asians, who instead do sport some notable Mainline European affinity.

It's also interesting that CEU are among the most North African related of all European populations.

Some prehistoric and proto-historic speculation

IF, and only IF, the affinity of Ötzi with Sardinians can be considered representative of how most Italy was in the Chalcolithic (and not a random fluke specific of that man or his mountain community), then, we should consider two further waves into Italy: (1) of West Asian affinity (maybe from the Agean since the Bronze Age or even before) and (2) of mainland European affinity (Indoeuropeans: Italics, Celts).

IF this is correct then the Ligures would not be so much descendant genetically from La Lagozza-Chassey, as I said above but from the "Aegean" wave. This would also be consistent with some individual Tuscans clustering with Southern Italians as well (historical Etruscans are one of the culminations of these Aegean waves together with the Greek colonies).

But sincerely, I am not aware of any such Aegean flow arriving to the proto-historical Liguria, are you?

So I must consider that there is another possibility: that the Sardinian element represents only one of several Neolithic (or maybe even Paleolithic but nothing clear here) elements in Italy, maybe associated to Y-DNA I2a (strong in Croatia, Bosnia, etc.), while the other, the one most akin to West Asia, would be related to Y-DNA E1b-V13 (strong in Greece and Albania) and maybe other patrilineages from the Eastern Mediterranean like J2b, etc. Both E1b-V13 and I2a are know from ancient DNA from the Neolithic of the Western Mediterranean, so they did indeed take part in these migrations.

Then the "Greek" or "Aegean" (or "Albanian" if you wish) component was reinforced by Bronze Age flows while the "Dalmatian" one was diluted instead by the successive Indoeuropean (Kurgan) waves.

20 comments:

"This confirms four clusters: Main European (green), Sardinian (red), West Asian (blue) and North African (purple).

Some prehistoric and proto-historic speculation"

My take would be

1) the red as the pre-IE Anatolian first farmers spreading west along the islands and coasts and also north along the atlantic coast (but maybe in smaller numbers?)

2) Followed by the West Asian (blue) IE coming afterwards partly following the original Anatolian route but also a second middle route along the danube and a third northern route as well.

(With the southern route more admixed with Anatolians the far north route more admixed with the greens and the middle route somewhere in between?)

3) If so the earlier Anatolian wave e.g. Otzi, Ligurians, Etruscans etc, would get squeezed from multiple directionsa) IE from the south and east (in Greek form) via the seab) IE from the north and east (in Italic form)via the danube / croatiac) Atlantic cowboys(?) from the west (in Gallic form) over the alpsd) (Atlantic cowboys + IE mix?) from the north (in Celtic form) over the alps

Hence why the first farmer layer only survived in isolated pockets.

#

The odd thing is the CEU / North Africa layer. I'd expect given my speculation the British Isles to be:Anatolian / Atlantic coast around the south and west combined with Germanic/Scandi/Celtic + IE from the east

I wonder if the North African signal is from an earlier layer that survived strongly in north Africa (protected by desert adaptation?) but who were mostly displaced elsewhere with a stronger signal in more peripheral areas where they could retreat to?

You had a picture of a Berber on one of your posts from a while ago and i almost mentioned at the time he looked like a darker version of a welsh mountain hobbit.

First, it is important to understand that the Admixture components are not actual populations but relations of affinity. A real prehistorical population may well be "made up" of two or more of those components but in their own apportions. For example when Dienekes analyzed the various known autosomal aDNA from Epipaleolithic and Neolithic Europe, they appeared as composites of various "zombie" components and never as "pure" anything (actually one does show "pure" in the K7 but I'm more thinking in the K12 in fact).

So we cannot imagine the components arriving as pure things. Instead, if I picture "West Asian farmer immigrants" here, I imagine them like Palestinians (for example) look: 60% blue but also 30% green, etc. They'd be Anatolian rather than Palestinian, so more green, less blue, maybe not too different from modern South Italians... and their "Ligur" relatives.

Your proposal implies massive replacements elsewhere in the World, up to the point that the Sardinian "red" component almost vanishes.

Regardless I cannot accept Anatolia for the origin of Indoeuropeans (much less after the Neolithic). For me it is 100% clear that the Indoeuropeans arrived from Russia in the Chalcolithic (much later for Italy and Western Europe) and they correspond with the Kurgan model. In the case of Italy there are two known waves: Italics in the 2nd millennium BCE (from Central Europe) and later Celts in the 3rd century BCE (also from Central Europe). The Italic invasion overlapped with the Etruscan one, which did indeed come from Anatolia but is not IE.

"First, it is important to understand that the Admixture components are not actual populations but relations of affinity. A real prehistorical population may well be "made up" of two or more of those components but in their own apportions."

Yes.

"Your proposal implies massive replacements elsewhere in the World, up to the point that the Sardinian "red" component almost vanishes."

If the model in my head is correct i think this is related to your first point. I think the "red" may represent the *relatively unadmixed* Anatolian segment in refuges like Liguria and Sardinia. I think the rest of the red component is part of the admixed coastal population.

(Also i wonder how far the red component had spread from the coast so any replacement may have been large in percentage terms but not very large in terms of geography. Basically i wonder if a lot of the later Greek trading settlements around the med were built on top of earlier "red" ones.)

"Regardless I cannot accept Anatolia for the origin of Indoeuropeans"

Fair enough. I think they came into Europe by three routes: coastal, danubian and kurgan in varying proportions and on different time scales and with the southern IE wave (Greek) overlapping with the Anatolian wave (Etruscan) so for me the exact origin doesn't have to be the same as the place that had the most impact. Even if Anatolia (or the Transcaucasus imo) was the ultimate origin if all three of Greece, Danube and Kurgan the three secondary origins then one of them could have had the biggest overall impact.

The problem I see with that is that it's built on thin air and absolutely nothing else. When we step on the ground, we can easily see that Sardinians and Anatolians (Turks) have almost nothing in common within the context of West Eurasia: in my December mini-study of West Eurasians, for example, at K=4 already, Sardinians are almost 100% in their own distinct component, shared almost nothing with Turks.

The populations that share the Sardinian component the most (at K=5 for example) are (in this order) Basques, Spaniards, Northern Italians, Tuscans, French, North Europeans, Orcadians...

It is true that this component (or variants of the same thing) was high among some Italian and Western European Neolithic peoples but that does not mean it comes from Anatolia. Actually the European Neolithic has only very thin, blurry, connections to Anatolia archaeologically speaking (instead in the Bronze Age, Anatolia, specially Troy, was much more influential but only in the Balcans and Italy).

In this Dienekes' K12 analysis of aDNA we can see how his Atlantic-Med component is high in La Braña, an Epipaleolithic Iberian. In this other one, it is also high in the Mediterranean component. We must understand therefore that when we talk of Mediterranean, Southern or Atlantic-Mediterranean we are with all likelihood talking of a native European component, not "Anatolian" (otherwise prove the "Anatolian" connection - I dare you).

"(or the Transcaucasus imo)"

The Caucasus, cis or trans, is a marginal region, forget it. It is receiver of genes, a refugium for rare clades no doubt but not any emitter of genes around the World. Archaeologically also it has limited relevance.

Anatolia is more important but let's not exaggerate. As far as I know, the European Neolithic began in Greece, not in Turkey. And it is among the oldest ones with pottery in all West Eurasia (East Asia had pottery before Neolithic). The Thessalian Neolithic is "young" for West Asian standards but not too much, just 2000 years more recent. Also the process of penetration into the Balcans, with two different cultures, may have incorporated aboriginal peoples, specially in the Cardium Pottery culture.

Forget about Anatolia, or at least relativize it a bit. Anatolia is overrated.

"We must understand therefore that when we talk of Mediterranean, Southern or Atlantic-Mediterranean we are with all likelihood talking of a native European component, not "Anatolian" (otherwise prove the "Anatolian" connection - I dare you)."

I agree except i think it's a mixture of native + some coastal Anatolian (e.g. Etruscan) + some coastal IE (Greek). I don't think the southern wave(s) penetrated very far from the coast but i think they were there.

"The Caucasus, cis or trans, is a marginal region"

I only disagree a little. I think the Transcaucasus may have been the ultimate origin of secondary heimats like Thessaly or Kurgan but i agree those secondary heimats are the sources of what came after.

An analogy of what i mean might be if you imagine England as the Transcaucasus and America as the Kurgan culture and the galaxy has been colonized from America and people were arguing over whether the English language started from England or America.

"I think the Transcaucasus may have been the ultimate origin of secondary heimats like Thessaly or Kurgan but i agree those secondary heimats are the sources of what came after".

You don't have any support at all for that kind of ideas. While there is a thin archaeological thread linking SW Anatolia Neolithic with Thessaly Neolithic and this may be consistent with a thin spread along the southern Anatolian strip of E1b-V13, which would then become a key marker for European Neolithic (after a marked founder effect in Greece and Albania), the Caucasus does not seem to have played any role at all ever.

Of course there's always new things to discover that my change our understanding but I'll wait for them instead of speculating in a void, thanks.

Also how come do you mix Thessaly Neolithic and Kurgan culture? They are among the two most unrelated things I can imagine.

"Also how come do you mix Thessaly Neolithic and Kurgan culture? They are among the two most unrelated things I can imagine."

Either Dionekes' "West Asian" component represents something real or it doesn't. If it doesn't the whole argument is moot. If it doesrepresent something real- it seems to have a concentration in Greece and Southern Italy tapering off as you continue along the coast- it seems to have a concentration in the balkans tapering off as you travel SE to NW along the danube- it seems to have a weaker concentration in the north / steppe region tapering off as it goes west

There's a lot of possible explanations for this but one is that people from the same original region moved separately by different routes to those three other regions and developed three separate heimats which despite all their other differences were linked by genetics and language to the original region.

If

"The Caucasus, cis or trans, is a marginal region"

is true then the only reason the people there might have spread far and wide (if they did) would have been the fluke of living adjacent to the first farmers. So if as a result of that fluke they expanded in disconnected small groups in various directions and ended up all over the place e.g. Tarim, Thessaly, steppe, Iran etc and once there developed material cultures adapted to those surroundings then you have a possible explanation why widely dispersed and very different populations could still be related by genetics and language family.

I'm not saying it is true but it seems plausible to me in the context of the early adopters of farming having a first-mover advantage.

The Caucasus or West Asian component is real but IMO it represents part of two different migration processes:

1. It is the bulk of the West Asian Neolithic input to SE Europe (and by extension to the rest of Europe in more diluted manner). Here it comes from Anatolia directly.

2. It is also present (probably) in the Kurgan flows but here it comes from SE European Russia (the Ciscaucasus if you wish).

How can this be possible? Because the component is actually dominant in all what I call Highland West Asia: the Caucasus, Anatolia, Iran, Kurdistan, being also important in Syria, Lebanon and Iraq (but these are transitional zones towards the Palestine and Arabia zones, which are at least two distinct genetic regions but that I have not studied yet in depth).

So D's "West Asian" component represents the bulk of all West Asian Neolithic and post-Neolithic genetic input by various routes. But that does not make Neolithic Thessaly and Samara valley directly related in any meaningful way.

I agree that each of the colors represents admixed populations, to varying degrees, and in different proportions. Still, the "redness" of Sardinia (and thus Ötzi) is striking, as is the amount of "green" throughout Italy - not just the North.

Regarding the latter, this indicates to me a strong Balkan connection. I.e., if "green" is post-LGM northern European (partially Balkan) and neolithic LBK (Balkan with some northern Anatolian), then the green in Italy can have both northern IE and attested later Balkan/Greek sources. All this would also would make the relatively high amount of green in the Levant more believable.

"Red" basically does not occur in the Levant, so it must be mostly paleolithic and isolated European Mediterranean. It is absolutely mind-boggling that North African is much larger than this in Northern Europeans. IMO, the only explanation is that "red" is not just mostly paleolithic Mediterranean, but also isolated and just one of (a few? several?) such populations. That is, in the past admixture between different groups and cultures was much lower than in historic times. There were regions of mostly "red" in Sardinia and parts of Italy, and there were regions that already looked different 5,000 years ago.

You may want to look at fig. S6, which shows the whole Admixture sequence from K=2 to K=9. Not big changes (because most of the new subdivisions happen in West Asia, showing that the choice of outgroups was quite poor) but at K=9 the main European component finally splits in two and one component (orange) is more Northerner and the other two (cobalt blue, purple) are more specifically Italian.

There is therefore some division between these regions but it is not too strong and hidden by the great West Asian diversity that for this study is pointless. I can conceive better designed exercises by not oversampling North Italians nor Sardinians, including comparisons with Turks, Greeks, Croats and Spaniards, as well as North Europeans but not with the transmediterranean examples used here, which are noisy and pointless. But well...

Regardless: the Green component probably represents several things (all coming from mainland Europe, not necessarily North: Romanians are not too different from, say, Germans genetically) and not just one, while I agree that the Red one is non-Asian but I'd doubt on considering it "Paleolithic" because it has been found in mostly Neolithic peoples (also in aDNA), even if its origin is European.

What we have to dispel is the confusing notion of Neolithic=West Asian. Of course some lineages and genetics must have arrived from West Asia with the Neolithic (and later also in the Bronze Age for example) but the European Neolithic is essentially a European phenomenon of Balcanic and (importantly) other origins and sub-origins, in which the West Asian influence existed (specially in the Balcans) but was necessarily limited.

So I think that the Red component is aboriginal European but of Neolithic expansion largely. Much needs to be researched yet to fully understand this matter but it may well have got an Adriatic origin.

I thought Tuscan genes were shown to have close relatives in northern anatolia, about five years ago in a genomic study. The implication was that Etruscans were refugee Hittites from the bronze age collapse. This is consistent with the Aegean wave you mention in your comments. Along those lines of thought, perhaps the Sardinians are the 'Sherdan' mentioned in Egyptian chronicles of the invasions of the Sea People. I suspect the Sherdan were not from Sardinia, but instead went to it, after they were repulsed from Egypt.

A tendency towards Turkey, not specifically any region in it however. That study was made on mtDNA, very specially ancient mtDNA from wealthy burials, although some other studies may have weakly supported that tendency for Etruscans in general (notice also that ancient Etruria and modern Tuscany only partly overlap).

Besides there is an archaeologically evident trend of growing Aegean influences in Southern and Central Italy since some moment in the Chalcolithic - add to that Etruscan and Greek colonization in the Bronze and Iron Ages.

... "perhaps the Sardinians are the 'Sherdan'"...

Probably not because the Sherden are depicted with horned helmets and that is not an archaeological item in the West. Instead it was common among Sumerians, while other such items seem Mycenean-like.

The most common notion today about the Sea Peoples is that the were Mycenaean Greeks and allies, who acted much like "Mediterranean Vikings" of sorts. Shardan could well be related to Sardes and therefore mean Lydians.

"I suspect the Sherdan were not from Sardinia, but instead went to it, after they were repulsed from Egypt".

No evidence for that other than a name coincidence. I rather suspect that the name Sardinia is just "sardine" (island of sardines for example) and that sardine has a Basque (Iberian?) etymology (sarda+gin: fish-school-maker, having been preserved in many different languages that way because originally Indoeuropeans had no words for sea fish).

Whatever the case Sardinia was not obviously invaded in the Bronze Age at all but it may have got strong links with the proto-Iberians instead ("nuraghe" and "motillas" are identical for example).

"Probably not because the Sherden are depicted with horned helmets and that is not an archaeological item in the West."

Not entirely relevant as it's figurines rather than helmets themselves but a site i was reading

http://people.usd.edu/~clehmann/erp/Sardinia/prehist.htm

has a Sardinian figurine at the bottom of the page with an odd helmet and googling "sardinia nuragic figurines" gets a ton of images including

http://www.flickr.com/photos/taurielloanimaliorchidee/6275820207/

which makes me think bulls horns.

I played a video game set in the Roman era where the Iberian faction had a unit of guys wearing bulls horn helmets. I thought it was a made-up fantasy unit but now i wonder if it might have been a real thing at least in a ritual context.

The bull connection, if it is bull's horns, make me think about the Minoans.

Fascinating, I was totally ignorant of that iconography. We can well say that the size of the horns makes the helmet not just incompatible with those depicted in Egypt but also unlikely to be used in real fights but, on the other side, the elements are very similar. So your case has gained a lot of weight, really.

"I played a video game set in the Roman era where the Iberian faction had a unit of guys wearing bulls horn helmets. I thought it was a made-up fantasy"...

There are many votive and decorative images from the Iberian period and nothing like that: it's a fantasy. There's arguably a moment when the iconography of the deer is replaced by that of the bull in South Iberian rock art (even in some cases making a bull out of a deer) but no helmets (and in this case I thread with more certainty than in Sardinia).

Actually the horns of the Sardinian Nuraghic helmets are clearly those of a goat, not any bull or cow, what reminded me of the S'Urtzu of Sardinian Carnivals and the identical Hartza (the bear) of Basque Carnivals, both of which are actually represented by goat heads as headdresses. See Insula #3 (p.41) for the carnivals and also Insula #5 (p.89) for how this kind of goat-horned bear-man figure was known in parts of Germany and other regions as Krampus, in complex connection with the myth of Santa Claus.

I was initially thinking bull's horns because of the size of the horns on the figurines and Egyptian depictions of Sherden but your point about the goat head-dress makes more sense and those horns are too small. However i then wondered if goat horns were always that small.

Anyway some semi-random googling later:

http://en.wikipedia.org/wiki/Horned_deity

http://en.wikipedia.org/wiki/Capra_(genus)

"Evidence of the ibex is widely present in the archaeological record, particularly in the Near East and Mediterranean regions."

http://purpleopurple.com/life-science/mammals/ibex.jpg

http://www.gvzoo.com/files/u2/Ibex.jpg

Makes me wonder if that's what the Sherden were wearing on their heads?

I don't know how well goat horns preserve but if Sherden did wear ibex head-dress then a testable prediction would be finding *pairs* of ibex horns close together fairly commonly in nuragic (and Iberian equivalent?) sites.

The Sherden helmets are clearly "bovine" in their style. It's also said that their general armor style was identical to that of the Peleset/Philistines, another Sea People who established themselves around Gaza, were Greek speakers and originated in Mycenaean Crete. The Shardans used naue II swords, the most advanced military tech of the Eastern Mediterranean in that period - I doubt such thing existed in Sardinia so early.

I wouln't go crazy about all that unless you plan to write historical fiction.

They would have ended there with their swords, right? AFAIK no naue II swords exist in the Western Med and the Sardinian Nuraghe culture both pre-dates and post-dates the Sea Peoples' period (1350-1275 for the mentions of the Sherden in Egypt, 1900-750 for the Nuraghe culture). So probably not.

However it's likely, IMO, that some Mycenaean Greeks ended up in Iberia, not founding anything nor giving name to anything probably but maybe waging some wars and doing some plunder, as narrated in some of the Heraklean works (and probably also reflected in Plato's narration of Atlantis). We know that they left a cultural impact very specially in SE Iberia, El Argar culture, where they began burying their death in the Greek style of pythoi (large jars) since c. 1500 BCE (in turn Greeks adopted on occasion the burial in tholoi, which probably originated in Chalcolithic Iberia - even if speculatively might have an ultimate Oriental origin).

But nothing specific that could relate the Sherden with Sardinia other than sound similitude. It may well be like relation "rose" with Russia, "fin" ("the end" in Spanish and Italian) with Finland, or Peru (Peter in Basque, one variant) with the country of Peru. These things happen all the time and you have absolutely nothing to link the two beyond that feeble speculation.

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